Exploring and Exploiting Epigenetic Plant Immunity

Crop protection is of crucial importance to the global food supply chain. Despite the major technological advances since the green revolution, plant diseases continue to pose a threat to food security. Aggravated by legislative restrictions on the use of pesticides and GM crops, there is an urgent need to develop alternative crop protection methods. This objective has become a key priority of the sustainable intensification agenda in the UK.

Quantitative disease resistance is an attractive concept for crop protection. Unlike qualitative resistance, which relies on single resistance genes, quantitative resistance depends on a multitude of interacting genes and mechanisms. Accordingly, it is more resilient against co-evolution by pathogens and offers broad-spectrum protection against multiple pathogen isolates and species. Despite these advantages, however, quantitative resistance has not been exploited to its full potential, because of its complex regulation and sometimes variable effectiveness compared to conventional protection strategies. For instance, while quantitative resistance slows down disease progression, it is often too weak to prevent infection by virulent pathogens completely.

Induced resistance (IR) is an adaptive immune response that allows plants to boost their innate level of quantitative resistance. IR typically develops after recovery from biotic stress and is based on a form of immune memory called priming, which enables a faster and/or stronger defence induction against future pathogen attack. We have previously shown that long-lasting IR in the model plant Arabidopsis has an epigenetic basis, involving genome-wide reductions in DNA methylation, which can be transmitted to subsequent generations. While epigenetic IR (epi-IR) after exposure to disease stress can be variable, we found that direct manipulation of the Arabidopsis epigenome can yield near complete levels of protection against downy mildew disease. The epigenetic loci controlling this artificial epi-IR response are stable over multiple generations and are not associated with major reductions in plant growth, making it attractive for exploitation in crop protection. However, crops have larger genomes than Arabidopsis, rendering them more vulnerable to genome-wide reductions in DNA methylation. Thus, to advance this research, we propose to develop a more precise and adjustable method to introduce epigenetic variation in plant genomes. This would not only be of high translational value to crop protection and breeding, but also represent a valuable research tool to explore the complex mechanisms by which epigenetically altered DNA loci prime defence genes.

Based on preliminary proof-of-concept results, our project will develop a novel tool for adjustable introduction of epigenetic variation in plant genomes, taking advantage of the expertise and resources in our labs. This adjustable epi-mutagenesis will be optimised for epi-IR against downy mildew disease in both Arabidopsis and lettuce. We will then use the method to screen Arabidopsis mutants impaired in epigenetic gene regulation for their ability to develop and retain epi-IR, followed by next-generation sequencing analyses to reveal the underpinning mechanisms on a genome-wide scale. In parallel, we will exploit our method by selecting for epigenetically modified lettuce lines with high levels of epi-IR against downy mildew disease. These lines will be characterised for commercially relevant traits and used to generate epigenetic recombinant inbred lines, in order to separate epi-IR from potentially undesirable effects on growth and seed set. The project will be conducted in partnership with ENZA, a global crop breeding company covering >50% of the lettuce seed market in the UK. This partnership will be supervised by a business development manager to ensure efficient knowledge exchange, manage intellectual property, and facilitate adoption of the technology by the industry partner.

Epigenetic mechanisms are emerging as multifaceted regulators of plant immunity. Previous research has shown that diseased plants can prime their offspring epigenetically to enable a more efficient defence response against pathogens. In the model plant species Arabidopsis, this epigenetic induced resistance (epi-IR) depends on active DNA demethylation by the DNA demethylase AtROS1. In addition, we have shown that artificial introgression of strongly hypomethylated DNA from the ddm1 mutant into the wild-type background of epigenetic recombinant inbred lines can yield near complete levels of epi-IR against downy mildew disease without concomitant reductions in plant growth. While this raises translational opportunities, crop species are typically more vulnerable to major reductions in DNA methylation than Arabidopsis, resulting in sterile or lethal phenotypes. The current project addresses this hurdle by developing a new tool that allows for dosed introduction of epigenetic variation in plant genomes. In partnership with the international seed company ENZA, we will optimise this adjustable epi-mutagenesis method for lettuce and select for lines expressing stable epi-IR against the downy mildew pathogen Bremia lactucae. In parallel, we will apply the adjustable epi-mutagenesis method to study the mechanisms by which hypomethylated DNA loci (epi-loci) prime defence gene expression in Arabidopsis against the downy mildew pathogen Hyaloperonospora arabidopsidis. To this end, we will compare the effects of increasing degrees of DNA hypomethylation on epi-IR between wild-type plants and mutants that are altered in epigenetic gene regulation. Subsequent genome-wide analysis of DNA methylation, (non)coding RNA and heterochromatic interactions, followed by targeted validation of candidate epi-loci through CRISPR-dCas-based reverse epigenetics methods, will allow us to identify the complex mechanisms by which DNA methylation controls defence gene expression and plant immunity.